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Equipment

Electrospray Ionization (ESI)

Please Note: This page is being updated to reflect equipment changes/updates!!

Ion Trap Mass Spectrometer (Thermo Electron LTQ)

This is the most sensitive mass spectrometer for identification of proteins with MS/MS capability. The sensitivity limit is low fmol of peptide and it can usually identify a protein if it is visible by silver-stained SDS-PAGE.

Ion Trap Mass Spectrometer (ThermoFinnigan LCQ Deca XP)

This is the older, 3D version of ion-trap, similar to the LTQ but less sensitive. It is still a powerful instrument for protein identification.

Tandem Quadruple Mass Spectrometer (Agilent 6460)

This instrument, also referred to as a triple quadrupole (or QQQ) brings high-throughput quantitative capabilities to the facility. The strength of these systems is not discovery, but rather quantification of known analytes of interest using Selective Reaction Monitoring (SRM) experiments. These may be thought of as "mass westerns", although the sensitivity of western blotting is normally better than SRM. A big advantage of SRM however is no antibody is required.

Matrix-Assisted Laser Desorption Ionization (MALDI)

MALDI TOF/TOF Mass Spectrometer (Applied Biosystems 4700)

This is a MALDI instrument with MS/MS capability. If you have good amount of peptide, a larger peptide (5,000 Da) might be sequenced. It also has high throughput MS/MS capability. We often perform LC-MALDI analyses on this system, it is also suitable for stable isotope experiments.

Peptide Sequencer

Applied Biosystems Procise cLC 494 and HT494

This is the automated Edman degradation protein sequencer. Edman degradation contributed to protein structural studies, especially sequencing for nearly 50 years since 1950. With the development of DNA sequence databases and mass spectrometry, its role in protein sequencing has faded significantly. However, if one would like to know the N-terminal sequence of a peptide/protein, this is the instrument to use. It requires 1-2 pmol but will give you definite answer. Mass spectrometry is very weak, almost powerless for the sequence determination of the N-terminus of a peptide/protein.